Filtering duplicates with MACS2 after re-sequencing a sample to increase read depth
I am analyzing a ChIP-seq dataset. In order to increase read depth and obtain enough uniquely mapped reads, I decided to re-sequenced my sample and merge that dataset with the data I already have. However, I am concerned that macs2 will call more duplicates and omit them during the peak calling step. Is there anyway to avoid this? Any help will be greatly appreciated.
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